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CCRGeneticsBranch / khanlab_ngs_pipeline

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Arriba error at draw_fusions_patch.R #23

Closed vinegang closed 1 year ago

vinegang commented 1 year ago

Xinyu is getting this error for several samples.

Example log

/data/khanlab2/processed_DATA/log/arriba.55422396.e

Error code /data/Clinomics/Tools/ngs_pipeline_4.2_dev/Resources/draw_fusions_patch.R: line 2: iinal_1_K2_n_5u_AND_2_K2_n_5_200u_AND_3_K2_t_5u_AND_4_K2_t_5_200_AND_5_K3_n_5u_AND_6_K3_n_5_200u_AND_7_K3_t_5u_AND_8_K3_t_5_200_AND_1_K_n_5u_AND_2_K_n_5_200u_AND_3_K_t_5u_AND_4_K_t_5_200.140-rnings: command not found /data/Clinomics/Tools/ngs_pipeline_4.2_dev/Resources/draw_fusions_patch.R: line 3: syntax error near unexpected token warn=1 /data/Clinomics/Tools/ngs_pipeline_4.2_dev/Resources/draw_fusions_patch.R: line 3: options(warn=1)

vinegang commented 1 year ago

Xinyu got a similar arriba error.

Drawing fusion #33: EHBP1:USP34 Drawing fusion #34: AOPEP:EIF4G3 Error: unexpected numeric constant in "message("Done")160." Execution halted [Wed Jan 4 01:54:22 2023]

This is caused due to message("Done")160.lim1000000.CDK11B.DAC.csv in the draw_fusions_patch.R script.

Solution:

Updated the R script to "message("Done")" as per the original fix

vinegang commented 1 year ago

Updated the R script and pushed changes to git